Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/TrackStyles.py @ 20:85971ec2a527 draft default tip

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 81d946d4544a4ea7e5b55f90caef971eca6abba0
author sargentl
date Fri, 21 Sep 2018 16:30:54 -0400
parents 62dee5369e80
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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19
62dee5369e80 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
sargentl
parents: 6
diff changeset
1 #!/usr/bin/env python2
6
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yating-l
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2 import os
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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3 import json
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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4 import logging
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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5 from mako.lookup import TemplateLookup
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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7 class TrackStyles(object):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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8 def __init__(self, tool_directory, species_folder, trackListFile, cssFolderName="css", cssFileName="custom_track_styles.css"):
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yating-l
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9 self.logger = logging.getLogger(__name__)
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yating-l
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10 self.tool_directory = tool_directory
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11 self.species_folder = species_folder
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yating-l
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12 self.trackList = trackListFile
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yating-l
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13 self.cssFolderName = cssFolderName
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yating-l
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14 self.cssFileName = cssFileName
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yating-l
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15 self.cssFilePath = self._createCssFile()
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16 self.cssTemplate = self._getCssTemplate()
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17 self._addCssToTrackList()
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20 def addCustomColor(self, feature_class_name, feature_color):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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21 with open(self.cssFilePath, 'a+') as css:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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22 htmlMakoRendered = self.cssTemplate.render(
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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23 label = feature_class_name,
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24 color = feature_color
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25 )
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26 css.write(htmlMakoRendered)
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yating-l
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27 self.logger.debug("create customized track css class: cssFilePath= %s", self.cssFilePath)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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30 def _createCssFile(self):
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yating-l
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31 cssFolderPath = os.path.join(self.species_folder, self.cssFolderName)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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32 cssFilePath = os.path.join(cssFolderPath, self.cssFileName)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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33 if not os.path.exists(cssFilePath):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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34 if not os.path.exists(cssFolderPath):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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35 os.mkdir(cssFolderPath)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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36 os.mknod(cssFilePath)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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37 os.chmod(cssFilePath, 0o755)
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38 return cssFilePath
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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yating-l
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40 def _getCssTemplate(self):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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41 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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42 output_encoding='utf-8', encoding_errors='replace')
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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43 cssTemplate = mylookup.get_template("custom_track_styles.css")
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
yating-l
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44 return cssTemplate
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yating-l
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47 def _addCssToTrackList(self):
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48 with open(self.trackList, 'r+') as track:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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49 data = json.load(track)
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yating-l
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50 css_path = os.path.join('data', self.cssFolderName, self.cssFileName)
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51 data['css'] = {'url': css_path}
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yating-l
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52 json_string = json.dumps(data, indent=4, separators=(',', ': '))
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yating-l
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53 track.seek(0)
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54 track.write(json_string)
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55 track.truncate()
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56 self.logger.debug("added customized css url to trackList.json")
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